Set up a breading station with three shallow dishes: Stir together the flour, salt, and black pepper in the first dish. Beat the 3 eggs in the second dish and add the breadcrumbs to the third dish.
Coat the manicotti in the flour, then dip it into the egg, letting any excess drip off. Finally, press into the breadcrumbs. Transfer to a baking sheet and repeat with the second manicotti.
Place breaded manicotti in deep fryer and cook for 3-4 minutes, or until temperature reaches 165°F. Remove from fryer transfer to a lined baking sheet.
Cut on a diagonal and serve with warmed marinara sauce, and garnish with small side salad.